diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ee86cce7c8..779b1221139 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,7 @@ Docs: https://docs.openclaw.ai
 - Agents/tool policy: preserve restrictive plugin-only allowlists instead of silently widening access to core tools, and keep allowlist warnings aligned with the enforced policy. (#58476) Thanks @eleqtrizit.
 - Telegram/native commands: clean up metadata-driven progress placeholders when replies fall back, edits fail, or local exec approval prompts are suppressed. (#59300) Thanks @jalehman.
 - Matrix: allow secret-storage recreation during automatic repair bootstrap so clients that lose their recovery key can recover and persist new cross-signing keys. (#59846) Thanks @al3mart.
+- Matrix/crypto persistence: capture and write the IndexedDB snapshot while holding the snapshot file lock so concurrent gateway and CLI persists cannot overwrite newer crypto state. (#59851) Thanks @al3mart.
 
 ## 2026.4.2
 
diff --git a/docs/channels/matrix.md b/docs/channels/matrix.md
index e8369240af0..46158f5fad7 100644
--- a/docs/channels/matrix.md
+++ b/docs/channels/matrix.md
@@ -422,6 +422,7 @@ OpenClaw currently provides that in Node by:
 - using `fake-indexeddb` as the IndexedDB API shim expected by the SDK
 - restoring the Rust crypto IndexedDB contents from `crypto-idb-snapshot.json` before `initRustCrypto`
 - persisting the updated IndexedDB contents back to `crypto-idb-snapshot.json` after init and during runtime
+- serializing snapshot restore and persist against `crypto-idb-snapshot.json` with an advisory file lock so gateway runtime persistence and CLI maintenance do not race on the same snapshot file
 
 This is compatibility/storage plumbing, not a custom crypto implementation.
 The snapshot file is sensitive runtime state and is stored with restrictive file permissions.
diff --git a/extensions/matrix/src/matrix/sdk.test.ts b/extensions/matrix/src/matrix/sdk.test.ts
index d9f869551ff..94cf76d9a27 100644
--- a/extensions/matrix/src/matrix/sdk.test.ts
+++ b/extensions/matrix/src/matrix/sdk.test.ts
@@ -1194,7 +1194,9 @@ describe("MatrixClient crypto bootstrapping", () => {
     const callsAfterStart = databasesSpy.mock.calls.length;
 
     await vi.advanceTimersByTimeAsync(60_000);
-    expect(databasesSpy.mock.calls.length).toBeGreaterThan(callsAfterStart);
+    await vi.waitFor(() => {
+      expect(databasesSpy.mock.calls.length).toBeGreaterThan(callsAfterStart);
+    });
 
     client.stop();
     const callsAfterStop = databasesSpy.mock.calls.length;
diff --git a/extensions/matrix/src/matrix/sdk/idb-persistence.lock-order.test.ts b/extensions/matrix/src/matrix/sdk/idb-persistence.lock-order.test.ts
new file mode 100644
index 00000000000..559b2dddc6c
--- /dev/null
+++ b/extensions/matrix/src/matrix/sdk/idb-persistence.lock-order.test.ts
@@ -0,0 +1,74 @@
+import "fake-indexeddb/auto";
+import fs from "node:fs";
+import os from "node:os";
+import path from "node:path";
+import { afterEach, beforeAll, beforeEach, describe, expect, it, vi } from "vitest";
+import { clearAllIndexedDbState, seedDatabase } from "./idb-persistence.test-helpers.js";
+
+const { withFileLockMock } = vi.hoisted(() => ({
+  withFileLockMock: vi.fn(
+    async <T>(_filePath: string, _options: unknown, fn: () => Promise<T>) => await fn(),
+  ),
+}));
+
+vi.mock("openclaw/plugin-sdk/infra-runtime", async (importOriginal) => {
+  const actual = await importOriginal<typeof import("openclaw/plugin-sdk/infra-runtime")>();
+  return {
+    ...actual,
+    withFileLock: withFileLockMock,
+  };
+});
+
+let persistIdbToDisk: typeof import("./idb-persistence.js").persistIdbToDisk;
+
+beforeAll(async () => {
+  ({ persistIdbToDisk } = await import("./idb-persistence.js"));
+});
+
+describe("Matrix IndexedDB persistence lock ordering", () => {
+  let tmpDir: string;
+
+  beforeEach(async () => {
+    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), "matrix-idb-lock-order-"));
+    withFileLockMock.mockReset();
+    withFileLockMock.mockImplementation(
+      async <T>(_filePath: string, _options: unknown, fn: () => Promise<T>) => await fn(),
+    );
+    await clearAllIndexedDbState();
+  });
+
+  afterEach(async () => {
+    await clearAllIndexedDbState();
+    fs.rmSync(tmpDir, { recursive: true, force: true });
+  });
+
+  it("captures the snapshot after the file lock is acquired", async () => {
+    const snapshotPath = path.join(tmpDir, "crypto-idb-snapshot.json");
+    const dbName = "openclaw-matrix-test::matrix-sdk-crypto";
+    await seedDatabase({
+      name: dbName,
+      storeName: "sessions",
+      records: [{ key: "room-1", value: { session: "old-session" } }],
+    });
+
+    withFileLockMock.mockImplementationOnce(async (_filePath, _options, fn) => {
+      await seedDatabase({
+        name: dbName,
+        storeName: "sessions",
+        records: [{ key: "room-1", value: { session: "new-session" } }],
+      });
+      return await fn();
+    });
+
+    await persistIdbToDisk({ snapshotPath, databasePrefix: "openclaw-matrix-test" });
+
+    const data = JSON.parse(fs.readFileSync(snapshotPath, "utf8")) as Array<{
+      stores: Array<{
+        name: string;
+        records: Array<{ key: IDBValidKey; value: { session: string } }>;
+      }>;
+    }>;
+    const sessionsStore = data[0]?.stores.find((store) => store.name === "sessions");
+    expect(sessionsStore?.records).toEqual([{ key: "room-1", value: { session: "new-session" } }]);
+  });
+});
diff --git a/extensions/matrix/src/matrix/sdk/idb-persistence.test-helpers.ts b/extensions/matrix/src/matrix/sdk/idb-persistence.test-helpers.ts
new file mode 100644
index 00000000000..077b2020e7a
--- /dev/null
+++ b/extensions/matrix/src/matrix/sdk/idb-persistence.test-helpers.ts
@@ -0,0 +1,88 @@
+export async function clearAllIndexedDbState(): Promise<void> {
+  const databases = await indexedDB.databases();
+  await Promise.all(
+    databases
+      .map((entry) => entry.name)
+      .filter((name): name is string => Boolean(name))
+      .map(
+        (name) =>
+          new Promise<void>((resolve, reject) => {
+            const req = indexedDB.deleteDatabase(name);
+            req.onsuccess = () => resolve();
+            req.onerror = () => reject(req.error);
+            req.onblocked = () => resolve();
+          }),
+      ),
+  );
+}
+
+export async function seedDatabase(params: {
+  name: string;
+  version?: number;
+  storeName: string;
+  records: Array<{ key: IDBValidKey; value: unknown }>;
+}): Promise<void> {
+  await new Promise<void>((resolve, reject) => {
+    const req = indexedDB.open(params.name, params.version ?? 1);
+    req.onupgradeneeded = () => {
+      const db = req.result;
+      if (!db.objectStoreNames.contains(params.storeName)) {
+        db.createObjectStore(params.storeName);
+      }
+    };
+    req.onsuccess = () => {
+      const db = req.result;
+      const tx = db.transaction(params.storeName, "readwrite");
+      const store = tx.objectStore(params.storeName);
+      for (const record of params.records) {
+        store.put(record.value, record.key);
+      }
+      tx.oncomplete = () => {
+        db.close();
+        resolve();
+      };
+      tx.onerror = () => reject(tx.error);
+    };
+    req.onerror = () => reject(req.error);
+  });
+}
+
+export async function readDatabaseRecords(params: {
+  name: string;
+  version?: number;
+  storeName: string;
+}): Promise<Array<{ key: IDBValidKey; value: unknown }>> {
+  return await new Promise((resolve, reject) => {
+    const req = indexedDB.open(params.name, params.version ?? 1);
+    req.onsuccess = () => {
+      const db = req.result;
+      const tx = db.transaction(params.storeName, "readonly");
+      const store = tx.objectStore(params.storeName);
+      const keysReq = store.getAllKeys();
+      const valuesReq = store.getAll();
+      let keys: IDBValidKey[] | null = null;
+      let values: unknown[] | null = null;
+
+      const maybeResolve = () => {
+        if (!keys || !values) {
+          return;
+        }
+        db.close();
+        const resolvedValues = values;
+        resolve(keys.map((key, index) => ({ key, value: resolvedValues[index] })));
+      };
+
+      keysReq.onsuccess = () => {
+        keys = keysReq.result;
+        maybeResolve();
+      };
+      valuesReq.onsuccess = () => {
+        values = valuesReq.result;
+        maybeResolve();
+      };
+      keysReq.onerror = () => reject(keysReq.error);
+      valuesReq.onerror = () => reject(valuesReq.error);
+    };
+    req.onerror = () => reject(req.error);
+  });
+}
diff --git a/extensions/matrix/src/matrix/sdk/idb-persistence.test.ts b/extensions/matrix/src/matrix/sdk/idb-persistence.test.ts
index 0c62f319583..d2bbf51e2d5 100644
--- a/extensions/matrix/src/matrix/sdk/idb-persistence.test.ts
+++ b/extensions/matrix/src/matrix/sdk/idb-persistence.test.ts
@@ -2,99 +2,19 @@ import "fake-indexeddb/auto";
 import fs from "node:fs";
 import os from "node:os";
 import path from "node:path";
+import {
+  drainFileLockStateForTest,
+  resetFileLockStateForTest,
+} from "openclaw/plugin-sdk/infra-runtime";
 import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
 import { persistIdbToDisk, restoreIdbFromDisk } from "./idb-persistence.js";
+import {
+  clearAllIndexedDbState,
+  readDatabaseRecords,
+  seedDatabase,
+} from "./idb-persistence.test-helpers.js";
 import { LogService } from "./logger.js";
 
-async function clearAllIndexedDbState(): Promise<void> {
-  const databases = await indexedDB.databases();
-  await Promise.all(
-    databases
-      .map((entry) => entry.name)
-      .filter((name): name is string => Boolean(name))
-      .map(
-        (name) =>
-          new Promise<void>((resolve, reject) => {
-            const req = indexedDB.deleteDatabase(name);
-            req.onsuccess = () => resolve();
-            req.onerror = () => reject(req.error);
-            req.onblocked = () => resolve();
-          }),
-      ),
-  );
-}
-
-async function seedDatabase(params: {
-  name: string;
-  version?: number;
-  storeName: string;
-  records: Array<{ key: IDBValidKey; value: unknown }>;
-}): Promise<void> {
-  await new Promise<void>((resolve, reject) => {
-    const req = indexedDB.open(params.name, params.version ?? 1);
-    req.onupgradeneeded = () => {
-      const db = req.result;
-      if (!db.objectStoreNames.contains(params.storeName)) {
-        db.createObjectStore(params.storeName);
-      }
-    };
-    req.onsuccess = () => {
-      const db = req.result;
-      const tx = db.transaction(params.storeName, "readwrite");
-      const store = tx.objectStore(params.storeName);
-      for (const record of params.records) {
-        store.put(record.value, record.key);
-      }
-      tx.oncomplete = () => {
-        db.close();
-        resolve();
-      };
-      tx.onerror = () => reject(tx.error);
-    };
-    req.onerror = () => reject(req.error);
-  });
-}
-
-async function readDatabaseRecords(params: {
-  name: string;
-  version?: number;
-  storeName: string;
-}): Promise<Array<{ key: IDBValidKey; value: unknown }>> {
-  return await new Promise((resolve, reject) => {
-    const req = indexedDB.open(params.name, params.version ?? 1);
-    req.onsuccess = () => {
-      const db = req.result;
-      const tx = db.transaction(params.storeName, "readonly");
-      const store = tx.objectStore(params.storeName);
-      const keysReq = store.getAllKeys();
-      const valuesReq = store.getAll();
-      let keys: IDBValidKey[] | null = null;
-      let values: unknown[] | null = null;
-
-      const maybeResolve = () => {
-        if (!keys || !values) {
-          return;
-        }
-        db.close();
-        const resolvedValues = values;
-        resolve(keys.map((key, index) => ({ key, value: resolvedValues[index] })));
-      };
-
-      keysReq.onsuccess = () => {
-        keys = keysReq.result;
-        maybeResolve();
-      };
-      valuesReq.onsuccess = () => {
-        values = valuesReq.result;
-        maybeResolve();
-      };
-      keysReq.onerror = () => reject(keysReq.error);
-      valuesReq.onerror = () => reject(valuesReq.error);
-    };
-    req.onerror = () => reject(req.error);
-  });
-}
-
 describe("Matrix IndexedDB persistence", () => {
   let tmpDir: string;
   let warnSpy: ReturnType<typeof vi.spyOn>;
@@ -108,6 +28,7 @@ describe("Matrix IndexedDB persistence", () => {
   afterEach(async () => {
     warnSpy.mockRestore();
     await clearAllIndexedDbState();
+    resetFileLockStateForTest();
     fs.rmSync(tmpDir, { recursive: true, force: true });
   });
 
@@ -171,4 +92,58 @@ describe("Matrix IndexedDB persistence", () => {
     const dbs = await indexedDB.databases();
     expect(dbs).toEqual([]);
   });
+
+  it("serializes concurrent persist operations via file lock", async () => {
+    const snapshotPath = path.join(tmpDir, "concurrent-persist.json");
+    await seedDatabase({
+      name: "openclaw-matrix-test::matrix-sdk-crypto",
+      storeName: "sessions",
+      records: [{ key: "room-1", value: { session: "abc123" } }],
+    });
+
+    await Promise.all([
+      persistIdbToDisk({ snapshotPath, databasePrefix: "openclaw-matrix-test" }),
+      persistIdbToDisk({ snapshotPath, databasePrefix: "openclaw-matrix-test" }),
+    ]);
+
+    expect(fs.existsSync(snapshotPath)).toBe(true);
+
+    const data = JSON.parse(fs.readFileSync(snapshotPath, "utf8"));
+    expect(Array.isArray(data)).toBe(true);
+    expect(data.length).toBe(1);
+  });
+
+  it("releases lock after persist completes", async () => {
+    const snapshotPath = path.join(tmpDir, "lock-release.json");
+    await seedDatabase({
+      name: "openclaw-matrix-test::matrix-sdk-crypto",
+      storeName: "sessions",
+      records: [{ key: "room-1", value: { session: "abc123" } }],
+    });
+
+    await persistIdbToDisk({ snapshotPath, databasePrefix: "openclaw-matrix-test" });
+
+    const lockPath = `${snapshotPath}.lock`;
+    expect(fs.existsSync(lockPath)).toBe(false);
+    await drainFileLockStateForTest();
+  });
+
+  it("releases lock after restore completes", async () => {
+    const snapshotPath = path.join(tmpDir, "lock-release-restore.json");
+    await seedDatabase({
+      name: "openclaw-matrix-test::matrix-sdk-crypto",
+      storeName: "sessions",
+      records: [{ key: "room-1", value: { session: "abc123" } }],
+    });
+
+    await persistIdbToDisk({ snapshotPath, databasePrefix: "openclaw-matrix-test" });
+    await clearAllIndexedDbState();
+    await drainFileLockStateForTest();
+
+    await restoreIdbFromDisk(snapshotPath);
+
+    const lockPath = `${snapshotPath}.lock`;
+    expect(fs.existsSync(lockPath)).toBe(false);
+    await drainFileLockStateForTest();
+  });
 });
diff --git a/extensions/matrix/src/matrix/sdk/idb-persistence.ts b/extensions/matrix/src/matrix/sdk/idb-persistence.ts
index d8b71d40712..238ab1d5b07 100644
--- a/extensions/matrix/src/matrix/sdk/idb-persistence.ts
+++ b/extensions/matrix/src/matrix/sdk/idb-persistence.ts
@@ -1,8 +1,27 @@
 import fs from "node:fs";
 import path from "node:path";
 import { indexedDB as fakeIndexedDB } from "fake-indexeddb";
+import type { FileLockOptions } from "openclaw/plugin-sdk/infra-runtime";
+import { withFileLock } from "openclaw/plugin-sdk/infra-runtime";
 import { LogService } from "./logger.js";
 
+// Advisory lock options for IDB snapshot file access. Without locking, the
+// gateway's periodic 60-second persist cycle and CLI crypto commands (e.g.
+// `openclaw matrix verify bootstrap`) can corrupt each other's state.
+// Use a longer stale window than the generic 30s default because snapshot
+// restore and large crypto-store dumps can legitimately hold the lock for
+// longer, and reclaiming a live lock would reintroduce concurrent corruption.
+const IDB_SNAPSHOT_LOCK_OPTIONS: FileLockOptions = {
+  retries: {
+    retries: 10,
+    factor: 2,
+    minTimeout: 50,
+    maxTimeout: 5_000,
+    randomize: true,
+  },
+  stale: 5 * 60_000,
+};
+
 type IdbStoreSnapshot = {
   name: string;
   keyPath: IDBObjectStoreParameters["keyPath"];
@@ -198,17 +217,22 @@ export async function restoreIdbFromDisk(snapshotPath?: string): Promise<boolean
   const candidatePaths = snapshotPath ? [snapshotPath] : [resolveDefaultIdbSnapshotPath()];
   for (const resolvedPath of candidatePaths) {
     try {
-      const data = fs.readFileSync(resolvedPath, "utf8");
-      const snapshot = parseSnapshotPayload(data);
-      if (!snapshot) {
-        continue;
+      const restored = await withFileLock(resolvedPath, IDB_SNAPSHOT_LOCK_OPTIONS, async () => {
+        const data = fs.readFileSync(resolvedPath, "utf8");
+        const snapshot = parseSnapshotPayload(data);
+        if (!snapshot) {
+          return false;
+        }
+        await restoreIndexedDatabases(snapshot);
+        LogService.info(
+          "IdbPersistence",
+          `Restored ${snapshot.length} IndexedDB database(s) from ${resolvedPath}`,
+        );
+        return true;
+      });
+      if (restored) {
+        return true;
       }
-      await restoreIndexedDatabases(snapshot);
-      LogService.info(
-        "IdbPersistence",
-        `Restored ${snapshot.length} IndexedDB database(s) from ${resolvedPath}`,
-      );
-      return true;
     } catch (err) {
       LogService.warn(
         "IdbPersistence",
@@ -227,14 +251,20 @@ export async function persistIdbToDisk(params?: {
 }): Promise<void> {
   const snapshotPath = params?.snapshotPath ?? resolveDefaultIdbSnapshotPath();
   try {
-    const snapshot = await dumpIndexedDatabases(params?.databasePrefix);
-    if (snapshot.length === 0) return;
     fs.mkdirSync(path.dirname(snapshotPath), { recursive: true });
-    fs.writeFileSync(snapshotPath, JSON.stringify(snapshot));
-    fs.chmodSync(snapshotPath, 0o600);
+    const persistedCount = await withFileLock(snapshotPath, IDB_SNAPSHOT_LOCK_OPTIONS, async () => {
+      const snapshot = await dumpIndexedDatabases(params?.databasePrefix);
+      if (snapshot.length === 0) {
+        return 0;
+      }
+      fs.writeFileSync(snapshotPath, JSON.stringify(snapshot));
+      fs.chmodSync(snapshotPath, 0o600);
+      return snapshot.length;
+    });
+    if (persistedCount === 0) return;
     LogService.debug(
       "IdbPersistence",
-      `Persisted ${snapshot.length} IndexedDB database(s) to ${snapshotPath}`,
+      `Persisted ${persistedCount} IndexedDB database(s) to ${snapshotPath}`,
     );
   } catch (err) {
     LogService.warn("IdbPersistence", "Failed to persist IndexedDB snapshot:", err);